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- PDB-3zkx: TERNARY BACE2 XAPERONE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 3zkx
TitleTERNARY BACE2 XAPERONE COMPLEX
Components
  • BETA-SECRETASE 2
  • XA4813
  • XA4815
KeywordsHYDROLASE
Function / homology
Function and homology information


memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis ...memapsin 1 / negative regulation of amyloid precursor protein biosynthetic process / melanosome membrane / melanosome organization / peptide hormone processing / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / trans-Golgi network / protein processing / glucose homeostasis / aspartic-type endopeptidase activity / endosome / Golgi apparatus / endoplasmic reticulum / proteolysis / membrane / plasma membrane
Similarity search - Function
Beta-secretase BACE2 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Beta-secretase BACE2 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Immunoglobulins / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
LAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsKuglstatter, A. / Banner, D.W. / Benz, J. / Bertschinger, J. / Burger, D. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Gsell, B. ...Kuglstatter, A. / Banner, D.W. / Benz, J. / Bertschinger, J. / Burger, D. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Gsell, B. / Hilpert, H. / Huber, W. / Kusznir, E. / Laeremans, T. / Matile, H. / Rufer, A. / Schlatter, D. / Steyeart, J. / Stihle, M. / Thoma, R. / Weber, M. / Ruf, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Mapping the Conformational Space Accessible to Bace2 Using Surface Mutants and Co-Crystals with Fab-Fragments, Fynomers, and Xaperones
Authors: Banner, D.W. / Gsell, B. / Benz, J. / Bertschinger, J. / Burger, D. / Brack, S. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Hennig, M. / Hilpert, H. / Huber, W. / ...Authors: Banner, D.W. / Gsell, B. / Benz, J. / Bertschinger, J. / Burger, D. / Brack, S. / Cuppuleri, S. / Debulpaep, M. / Gast, A. / Grabulovski, D. / Hennig, M. / Hilpert, H. / Huber, W. / Kuglstatter, A. / Kusznir, E. / Laeremans, T. / Matile, H. / Miscenic, C. / Rufer, A. / Schlatter, D. / Steyeart, J. / Stihle, M. / Thoma, R. / Weber, M. / Ruf, A.
History
DepositionJan 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-SECRETASE 2
B: XA4813
C: XA4815
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7205
Polymers68,6073
Non-polymers1142
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-19.6 kcal/mol
Surface area25200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.367, 153.829, 247.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein BETA-SECRETASE 2 / ASPARTIC-LIKE PROTEASE 56 KDA / ASPARTYL PROTEASE 1 / ASP1 / ASP 1 / BETA-SITE AMYLOID PRECURSOR ...ASPARTIC-LIKE PROTEASE 56 KDA / ASPARTYL PROTEASE 1 / ASP1 / ASP 1 / BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 2 / BETA-SITE APP CLEAVING ENZYME 2 / DOWN REGION ASPARTIC PROTEASE / DRAP / MEMAPSIN-1 / MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 1 / THETA-SECRETASE / BACE2


Mass: 42047.355 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR, RESIDUES 75-460 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y5Z0, memapsin 1

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Antibody , 2 types, 2 molecules BC

#2: Antibody XA4813


Mass: 13152.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PMESY4 / Production host: ESCHERICHIA COLI (E. coli)
#3: Antibody XA4815


Mass: 13406.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PMESY4 / Production host: ESCHERICHIA COLI (E. coli)

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Non-polymers , 3 types, 313 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.39 Å3/Da / Density % sol: 71.96 % / Description: NONE
Crystal growpH: 7 / Details: 0.2M SODIUM MALONATE, 20% PEG3350, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→34.7 Å / Num. obs: 49549 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 67.97 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.4
Reflection shellResolution: 2.37→2.5 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 1.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZKQ

3zkq


Resolution: 2.37→34.7 Å / Cor.coef. Fo:Fc: 0.9416 / Cor.coef. Fo:Fc free: 0.9389 / SU R Cruickshank DPI: 0.176 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.155
RfactorNum. reflection% reflectionSelection details
Rfree0.2085 2502 5.07 %RANDOM
Rwork0.1849 ---
obs0.1861 49387 99.59 %-
Displacement parametersBiso mean: 66.58 Å2
Baniso -1Baniso -2Baniso -3
1-9.9482 Å20 Å20 Å2
2---15.4095 Å20 Å2
3---5.4613 Å2
Refine analyzeLuzzati coordinate error obs: 0.359 Å
Refinement stepCycle: LAST / Resolution: 2.37→34.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 5 311 4857
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014651HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.166313HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1547SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes101HARMONIC2
X-RAY DIFFRACTIONt_gen_planes689HARMONIC5
X-RAY DIFFRACTIONt_it4651HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion18.44
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion605SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5028SEMIHARMONIC4
LS refinement shellResolution: 2.37→2.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 183 5.13 %
Rwork0.2682 3382 -
all0.2684 3565 -
obs--99.59 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8988-0.44931.09250.6146-0.74242.1618-0.0378-0.1349-0.1532-0.0517-0.0324-0.1111-0.08660.16470.0701-0.01780.00960.037-0.03780.1858-0.0609-24.576-24.111434.8618
23.1443-1.1742-0.10232.24-1.41813.5588-0.08610.0406-0.09380.15380.1050.099-0.0491-0.1575-0.0189-0.17240.0154-0.01860.09750.3014-0.0474-16.5003-39.168766.7277
34.47181.0763-1.03053.9115-0.00022.9267-0.1364-0.2594-0.25590.13840.0272-0.3259-0.04780.38680.1093-0.0089-0.0011-0.022-0.1296-0.0402-0.1125-12.6534-11.5714-7.8228
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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